usage: prog [options] <name of refinement directory> <iteration number>
This program will extract the necessary parameters from an EMAN2 refinement and create a card file (card.txt)
and a particle meta data file in the correct formats for FreAlign.
Examples:
The Eman2 refinement directory is refine_04 and the iteration you want to use within it is the 7th iteration:
e2refinetofrealign.py refine_04 7
[-] [-] [-] [- MODE] [-] [-] [-] [- RESLOW] [- RESHIGH] [- RREC]
[- RCLAS] [- THRESH] [- MASS] [- INTERP] [- RANDOMIZEMODEL] [- IMEM]
[- VERBOSE] [- PPID]
[positionalargs ...]
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --mode | str | Mode to run FreAlign in: Mode 1 - Refinement and Reconstruction, Mode 3 - Simple Search and Refinement |
| --fbeaut | None | (T/F)Apply extra real space symmetry averaging and masking to beautify final map prior to output |
| --ffilt | None | (T/F)Apply Single Particle Wiener filter to final reconstruction |
| --fstat | None | (T/F)Calculate additional statistics in resolution table at end (QFACT, SSNR, CC, etc.). T Uses more than 50 percent more memory. |
| --reslow | float | Resolution of the data included in the alignment. This is the low resolution value. ex:200 |
| --reshigh | float | Resolution of the data included in the alignment. This is the high resolution value. ex:25 |
| --rrec | float | Resolution of reconstruction in angstroms. It is the resolution to which the reconstruction is calculated. |
| --rclas | float | High resloution limit used for classification |
| --thresh | float | Phase Residual cutoff. Particles with a higher phase residual will not be included in the refinement |
| --mass | float | The ~mass of the particle in kilodaltons |
| --interp | str | Type of interpolation: 0 - Nearest Neighbor, 1 - Trilinear Interpolation (More Time-Consuming) |
| --randomizemodel | None | Optionally randomize the phases of the initial model to this resolution (in Angstroms) |
| --imem | str | Memory Usage: 0 - Least Memory, 3 - Most memory |
| --verbose | int | Level of verbose; how much information do you want the program to output?(0-9) |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
For more information go to emanwiki/EMAN2/Programs/e2refinetofrealign.